I don't believe this. There are tons of Software Engineer jobs paying around 80-100k in SF. That salary, in that city, puts you firmly in the middle class.
However, I agree with this piece. The tech companies and the people of San Francisco as a whole need to really change things. A big part of that change probably needs to happen at the local government level where there is so much incompetence and a decent amount of corruption: http://www.sfweekly.com/2009-12-16/news/the-worst-run-big-ci...
SF wants to be a big city, but many of the residents are actively refusing policies that will allow for better services, denser urban areas and other benefits of being a large city. Otherwise, San Francisco will continue to be the largest small town in America, with problems like homelessness and income inequality worse than a city ten times it's size (say, New York City).